We have been developing approaches for the MALDI-based analysis of proteins whose primary structures are known. An early challenge seriously approached in this Facility was the location of phosphorylation sites. Software has been developed to predict possible m/z values of ions that would be formed in MALDI, representing target components which are the products of digestion. In this program, the primary sequence of the peptide is provided or exported from a database. The program provides options for enzyme-specific cleavage sites, and either produces the fragments expected from complete digestion or a mixture of masses representing products of partial digestion. If the presence of phosphate groups is suggested, the user can indicate which residues are expected to be phosphorylated. The program then computes the masses of all possible digestion fragments, for all combinations of phosphorylation possibilities. Program development has now moved to computing proteolytic fragments when the protein contains various numbers of disulfide bonds. In addition to providing results in tabular form, these programs also generate "synthetic" mass spectra in a file format compatible with the MALDI data system, such that real data and simulated mass spectra can be viewed simultaneously on the computer screen. This has been found to greatly facilitate spectral analysis.